Some Informations about the projekt here would be really nice.
Q: Is there a dependence on the size of the gene tree, i.e., the number of species and genes? ?
Short description of the task at hand.
| Group | Duplication_Rate | Loss_Rate | HGT_Rate | Slope | Intercept | Spearman_Corr |
|---|---|---|---|---|---|---|
| P0 | 0.25 | 0.25 | 0.25 | 0.0014 | 0.23 | 0.21 |
| P1 | 0.50 | 0.50 | 0.50 | -0.0009 | 0.39 | 0.05 |
| P2 | 0.50 | 0.50 | 1.00 | -0.0012 | 0.48 | -0.02 |
| P3 | 0.50 | 0.50 | 1.50 | -0.0021 | 0.58 | -0.16 |
| P4 | 1.00 | 1.00 | 0.50 | -0.0011 | 0.40 | 0.04 |
| P5 | 1.00 | 1.00 | 1.00 | -0.0016 | 0.53 | -0.14 |
| P6 | 1.50 | 1.50 | 1.50 | -0.0016 | 0.57 | -0.24 |
Each plot needs a short discription. This can be done here. Maybe it is better not to iterate over the goups. maybe we should split the following coe into \(7\) seperate sektions, so we can write a custom text for each. But I guess an overall discription is fine as well... less work ;)
Some text here. . .
Each plot needs a short discription. This can be done here. Maybe it is better not to iterate over the groups. Maybe we should split the following code into \(7\) seperate sektions, so we can write a custom text for each.
| Group | Duplication_Rate | Loss_Rate | HGT_Rate | Slope | Intercept | Spearman_Corr |
|---|---|---|---|---|---|---|
| P0 | 0.25 | 0.25 | 0.25 | 0.0015 | 0.23 | 0.09 |
| P1 | 0.50 | 0.50 | 0.50 | 0.0004 | 0.34 | 0.04 |
| P2 | 0.50 | 0.50 | 1.00 | 0.0004 | 0.42 | 0.02 |
| P3 | 0.50 | 0.50 | 1.50 | -0.0022 | 0.55 | -0.09 |
| P4 | 1.00 | 1.00 | 0.50 | 0.0002 | 0.34 | 0.02 |
| P5 | 1.00 | 1.00 | 1.00 | -0.0016 | 0.49 | -0.04 |
| P6 | 1.50 | 1.50 | 1.50 | 0.0001 | 0.46 | 0.00 |
Each plot needs a short discription. This can be done here. Maybe it is better not to iterate over the groups. Maybe we should split the following code into \(7\) seperate sections, so we can write a custom text for each. But I guess an overall discription is fine as well... less work ;)
Some text here. . .
How does the fraction depend on the rate of duplications and losses for a fixed horizontal transfer rate?
Some text was was done here. And maybe why?
Short introduction
Boxplot of the Fraction of Xenologs plotted against the duplication rate with a fixed horizontal gene transfer (HGT) rate. The different colors marking the groups with the same HGT rate.
In XX we see examples of plotting in R. Explanation of the graph
Short introduction
Boxplot of the Fraction of Xenologs plotted against the loss rate with a fixed horizontal gene transfer (HGT) rate. The different colors marking the groups with the same HGT rate.
In XX we see examples of plotting in R. Explanation of the graph
How does the fraction depend on the horizontal transfer rate on the the rate of duplications and losses?
How does the fraction depend on the horizontal transfer rate with a fixed duplication and loss rate? --> fixed Question??
DIE PLOTS SIND NICHT ZUFRIEDENSTELLEND. PAUL HAST DU EINE TOLLE IDEE WIE WIR DAS GUT DARSTELLEN KÖNNEN
Ab Zeile \(205-258\) im tree_analyze.RScript falls da jmd rumexperimentieren mag. Überschrift "To-Do"
Boxplot of the Fraction of Xenologs plotted against the loss rate with a fixed horizontal gene transfer (HGT) rate. The different colors marking the groups with the same HGT rate.
DIE PLOTS SIND NICHT ZUFRIEDENSTELLEND. PAUL HAST DU EINE TOLLE IDEE WIE WIR DAS GUT DARSTELLEN KÖNNEN
Boxplot of the Fraction of Xenologs plotted against the loss rate with a fixed horizontal gene transfer (HGT) rate. The different colors marking the groups with the same HGT rate.
How does the fraction depend on the frequency of multifurctions.
AUCH HIER GEFÄLLT MIR DER PLOTT ÜBERHAUPT NICHT. BOXPLOT ÜBER ALLE GRUPPEN? ODER 6 EINZELNE PLOTS FÜR JEDE GRUPPE MIT LINEAREM ODER x^2 MODEL? ODER WIR BILDEN "BUCKETS" MIT x=NON_BINARY_PROB VS y=FRACTION_OF_XENOLOGS. und wir bilden buckets mit 1 = [0-0.1], 2 = [0.1-0.2], 3 = [0.2-0.3] usw..
caption = "Wasn hier zu sehen??"
plot(x = treeDataDf$non_binary_prob,
y = treeDataDf$Fraction_of_Xenologs)
Wasn hier zu sehen??
Second we consider the dependencies for the edges in Fitch graphs computed from an LDT graph. Here the following variants should be considered:
AsymmeTree).@@Paul, hast du hier nicht schonmal was angefangen?
In meinem Script finde ich dazu nichts.
Die können hier eingefügt werden
The triple set \(T (G)\) is related to the gene tree, while the triple set \(S(G, σ)\) is related to the species tree. It is therefore of interest to compare to what extent \(T (G)\) and \(S(G, σ)\) overlap the triple sets of true gene tree and the triple set of the true species tree, respectively. How can this be quantified in a meaningful way? Again we are interested in the dependence of the simulation parameters.
| Group | recall_cd_mean_100 | recall_cd_mean_80 | recall_cd_mean_60 | recall_cd_mean_40 | recall_cd_mean_20 |
|---|---|---|---|---|---|
| P0 | 0.67 | 0.66 | 0.65 | 0.61 | 0.50 |
| P1 | 0.67 | 0.66 | 0.64 | 0.59 | 0.51 |
| P2 | 0.67 | 0.66 | 0.66 | 0.63 | 0.56 |
| P3 | 0.70 | 0.70 | 0.68 | 0.65 | 0.58 |
| P4 | 0.64 | 0.63 | 0.63 | 0.58 | 0.49 |
| P5 | 0.69 | 0.69 | 0.68 | 0.65 | 0.56 |
| P6 | 0.69 | 0.68 | 0.67 | 0.64 | 0.61 |
| Group | precision_cd_mean_100 | precision_cd_mean_80 | precision_cd_mean_60 | precision_cd_mean_40 | precision_cd_mean_20 |
|---|---|---|---|---|---|
| P0 | 0.85 | 0.86 | 0.89 | 0.88 | 0.87 |
| P1 | 0.88 | 0.88 | 0.91 | 0.91 | 0.90 |
| P2 | 0.91 | 0.92 | 0.93 | 0.93 | 0.94 |
| P3 | 0.94 | 0.95 | 0.95 | 0.96 | 0.96 |
| P4 | 0.86 | 0.87 | 0.88 | 0.88 | 0.89 |
| P5 | 0.93 | 0.93 | 0.94 | 0.94 | 0.93 |
| P6 | 0.95 | 0.95 | 0.95 | 0.95 | 0.97 |
| Group | accuracy_cd_mean_100 | accuracy_cd_mean_80 | accuracy_cd_mean_60 | accuracy_cd_mean_40 | accuracy_cd_mean_20 |
|---|---|---|---|---|---|
| P0 | 0.97 | 0.98 | 0.98 | 0.99 | 1.00 |
| P1 | 0.95 | 0.96 | 0.98 | 0.99 | 1.00 |
| P2 | 0.93 | 0.95 | 0.97 | 0.98 | 1.00 |
| P3 | 0.92 | 0.94 | 0.96 | 0.98 | 0.99 |
| P4 | 0.94 | 0.96 | 0.97 | 0.99 | 1.00 |
| P5 | 0.93 | 0.95 | 0.97 | 0.98 | 1.00 |
| P6 | 0.92 | 0.94 | 0.96 | 0.98 | 0.99 |
| Group | recall_rs_mean_100 | recall_rs_mean_80 | recall_rs_mean_60 | recall_rs_mean_40 | recall_rs_mean_20 |
|---|---|---|---|---|---|
| P0 | 0.70 | 0.67 | 0.65 | 0.62 | 0.51 |
| P1 | 0.71 | 0.69 | 0.65 | 0.59 | 0.53 |
| P2 | 0.73 | 0.70 | 0.69 | 0.66 | 0.58 |
| P3 | 0.75 | 0.74 | 0.72 | 0.67 | 0.60 |
| P4 | 0.70 | 0.66 | 0.66 | 0.60 | 0.52 |
| P5 | 0.74 | 0.73 | 0.71 | 0.67 | 0.58 |
| P6 | 0.75 | 0.74 | 0.72 | 0.68 | 0.64 |
| Group | precision_rs_mean_100 | precision_rs_mean_80 | precision_rs_mean_60 | precision_rs_mean_40 | precision_rs_mean_20 |
|---|---|---|---|---|---|
| P0 | 0.83 | 0.83 | 0.84 | 0.86 | 0.85 |
| P1 | 0.85 | 0.85 | 0.86 | 0.88 | 0.89 |
| P2 | 0.91 | 0.89 | 0.91 | 0.91 | 0.93 |
| P3 | 0.92 | 0.93 | 0.93 | 0.94 | 0.95 |
| P4 | 0.86 | 0.84 | 0.86 | 0.84 | 0.90 |
| P5 | 0.91 | 0.91 | 0.91 | 0.92 | 0.92 |
| P6 | 0.94 | 0.93 | 0.94 | 0.94 | 0.95 |
| Group | accuracy_rs_mean_100 | accuracy_rs_mean_80 | accuracy_rs_mean_60 | accuracy_rs_mean_40 | accuracy_rs_mean_20 |
|---|---|---|---|---|---|
| P0 | 0.97 | 0.97 | 0.98 | 0.99 | 1.00 |
| P1 | 0.95 | 0.96 | 0.97 | 0.99 | 1.00 |
| P2 | 0.94 | 0.95 | 0.97 | 0.98 | 1.00 |
| P3 | 0.93 | 0.95 | 0.97 | 0.98 | 0.99 |
| P4 | 0.95 | 0.96 | 0.97 | 0.99 | 1.00 |
| P5 | 0.94 | 0.95 | 0.97 | 0.98 | 1.00 |
| P6 | 0.93 | 0.95 | 0.96 | 0.98 | 0.99 |
Sinvolle beschreibung des Plottes hier
Sinvolle beschreibung des Plottes hier
Sinvolle beschreibung des Plottes hier
Sinvolle beschreibung des Plottes hier
Sinvolle beschreibung des Plottes hier
Sinvolle Beschreibung des Plottes hier
Hier stimmt was mit den Daten nicht so ganz. Über all \(1\) drin.
Beschreibender Text hier.
Summary Table Recall
| Group | T_LDT_Recall_Mean | T_LDT_Recall_Median | S_LDT_Recall_Mean | S_LDT_Recall_Median |
|---|---|---|---|---|
| P0 | 1 | 1 | 1 | 1 |
| P1 | 1 | 1 | 1 | 1 |
| P2 | 1 | 1 | 1 | 1 |
| P3 | 1 | 1 | 1 | 1 |
| P4 | 1 | 1 | 1 | 1 |
| P5 | 1 | 1 | 1 | 1 |
| P6 | 1 | 1 | 1 | 1 |
Beschreibender Text hier.
Precision Summary
| Group | T_LDT_Precision_Mean | T_LDT_Precision_Median | S_LDT_Precision_Mean | S_LDT_Precision_Median |
|---|---|---|---|---|
| P0 | 0.05 | 0.01 | 0.07 | 0.00 |
| P1 | 0.09 | 0.04 | 0.10 | 0.04 |
| P2 | 0.13 | 0.09 | 0.18 | 0.11 |
| P3 | 0.14 | 0.10 | 0.23 | 0.18 |
| P4 | 0.09 | 0.04 | 0.10 | 0.04 |
| P5 | 0.12 | 0.08 | 0.17 | 0.11 |
| P6 | 0.14 | 0.10 | 0.20 | 0.13 |
Accuracy Beschreibender Text hier.
Accuracy Summary
| Group | T_LDT_Precision_Mean | T_LDT_Precision_Median | S_LDT_Precision_Mean | S_LDT_Precision_Median |
|---|---|---|---|---|
| P0 | 0.05 | 0.01 | 0.07 | 0.00 |
| P1 | 0.09 | 0.04 | 0.10 | 0.04 |
| P2 | 0.13 | 0.09 | 0.18 | 0.11 |
| P3 | 0.14 | 0.10 | 0.23 | 0.18 |
| P4 | 0.09 | 0.04 | 0.10 | 0.04 |
| P5 | 0.12 | 0.08 | 0.17 | 0.11 |
| P6 | 0.14 | 0.10 | 0.20 | 0.13 |
Recall: Beschreibender Text hier.
Precision: Beschreibender Text hier.
Accuracy: Beschreibender Text hier.
Tripple T Fraction: Beschreibender Text hier.
Tripple S Fraction: Beschreibender Text hier.